The three-member Select Board in Reading, population 666, thought Tropical Storm Irene was history.

Then it began to pen an update for this month’s annual report: “We are pleased to write that all of the repairs to roads, culverts and bridges damaged by Irene have been completed.”

Just not all permitted or paid for, it continues. The Federal Emergency Management Agency recently told Reading it lacked approval for some of the work. That, in turn, has delayed the Windsor County town from receiving some $600,000 in expected reimbursement — a shortfall bigger than the $531,755 in taxes proposed to fund the municipality’s entire general budget for the coming fiscal year.

From northwesternmost Alburgh to southeasternmost Vernon, flip through many Vermont town meeting reports this season and you’ll find communities flooded by the weather in 2011 and cleanup costs in 2012 are still mopping up the financial fallout in 2013.

“The storms and calamity that marked the beginning of fiscal year 2012 finally subsided — at least the storms did,” begins the Select Board in Dummerston, population 1,864. “The calamity continued, but it was more of a bureaucratic nature than of Mother Nature.”

The three-member Select Board in Halifax, population 728, is still tangling with federal and state paperwork to pay off Irene repairs approaching $4 million — five times its annual municipal budget.

“The fiscal year 2012 budget deficit is largely due to Irene,” it writes. “Work and project financial closeouts will continue in fiscal year 2013 and possibly beyond.”

Cavendish, population 1,367, uses its report to explain the statewide process for covering its more than $3 million in local damage: “FEMA reimbursements for qualified expenses are 90 percent (usually it is 75 percent) and the state adds another 5 percent to leave a net expense to the town of 5 percent.”

The state Legislature, for its part, has capped local financial liability for cleanup and restoration to no more than 3 percent of a municipality’s 2011 tax rolls. Almost 50 communities have borrowed money while they determine how to pay off repair bills, the Vermont League of Cities and Towns says. Most figured that federal and state reimbursement would come shortly after reconstruction.

Most figured wrong.

‘The real cost’

Wilmington, population 1,876, was the hardest-hit Vermont town, with more than $13 million in Irene damage. But it’s just one of dozens throughout the state facing the same problem.

“We have some items that we believe will be covered in full by FEMA but haven’t received the final approval on,” local leaders write. “The state has held back their portion of the payment until the final closeout is done for all projects. We are also waiting on the last payment from our insurance company. Once all these are finalized, we will know what the real cost will be to the town.”

Rockingham, population 5,282, devotes two full report pages to detailing both its nearly $4 million in damage — starting with the Bartonsville Covered Bridge washout seen by a half-million YouTube viewers — and a lingering shortfall of nearly $500,000.

“In last year’s report the town was still waiting for determination from FEMA on debris removal and reimbursement,” its Select Board writes 12 months later. “As of this report, the town has not yet received a determination.”

Bethel, population 2,030, saw the storm damage 60 of its 70 miles of local highway and destroy the machinery that powers its wells and wastewater treatment plant — leaving more than $8 million in bills. But two years later, taxpayers still don’t know what it will ultimately cost them.

“The financial consequences of Irene will likely not be realizable,” its Select Board writes, “until the time of budget preparations for the town’s fiscal year 2015.”

Such uncertainty is trickling down to other spending, as seen in dozens of the nearly 150 reports on file at the Vermont secretary of state’s office.

Westminster, population 3,178, already was facing years of loan payments due to its 2009 decision to buy the town’s former post office for $112,000. Then Irene racked up public infrastructure damage of $1.3 million, leading to “difficult budgetary choices,” as the town can barely afford to cover interest on its outstanding loans, let alone try to pay them off.

Pawlet, population 1,477, is one of many towns seeking money any way it can.

“A culvert on Betts Bridge Road was installed with Hazard Mitigation Grant Program funds,” it reports. “Bridge #6 on Route 153 on Town Highway #1 has been refurbished through a VTrans Structures Grant. Rafter Road has been rebuilt and all culverts replaced through Local Roads Grants. The town has been able to repair additional damage resulting from Irene through the Select Board working with FEMA.”

‘A job itself’

But for many communities, that challenge is as unprecedented as the storm.

Listen to leaders in Grafton, population 679, as they fill out paperwork to pay off $5.2 million in Irene repairs to 45 of the town’s 55 miles of roads: “For a few it seems like it will never go away, as a small group at the Town Hall continues to work through the FEMA process.”

And Ira, population 432, which thought it was spared with only $55,000 in damage: “The paperwork involved with FEMA was a job itself. Every dollar spent for stone, gravel, equipment, etc., had to be documented and separated and attached to each project that was done in town. This was actually harder than performing the road repairs.”

And Strafford, population 1,098, which has juggled 60 separate worksheets in hopes of recovering $2.7 million in cleanup costs: “I actually anticipate,” the town clerk writes, “that we will not be done with Irene until late 2014.”

Townshend, population 1,232, has gone to court to challenge FEMA for not paying for an upgraded Dam Road culvert required by the state Agency of Natural Resources.

“This matter is being appealed for a second time — this time by the Vermont attorney general — as a test case for all the towns in Vermont that have been left in the same position,” local leaders write.

In Sharon, population 1,502, the three-member Select Board and four-man road crew are adding their support.

“Sharon has joined with the state and numerous towns to appeal decisions made at the federal level we can only describe as unnecessarily bureaucratic, wrong-headed, capricious and — in many cases — many times more costly and which are needlessly made vulnerable to future damage with concomitant risk to people, property and the environment.”

‘A wake-up call’

Shrewsbury, population 1,056, is a bit more conciliatory as it awaits its own litigation on culvert costs: “2012 was the year for paperwork. 2013 promises more of the same. We ask for your continued patience with progress (or lack thereof).”

Not all communities are complaining. Woodbury, population 906, sustained more than $400,000 in damage yet only had to pay “a remarkable $2,600” because of federal and state reimbursement.

Fletcher, population 1,277, watched 2011 winter snow flatten its town garage and spring rain flood its roads before Irene hit. Last year’s report lamented that FEMA had changed its promised compensation estimates from $427,000 to $350,000. This year it received a final figure of $413,000, leaving a surplus approaching $50,000.

Orwell, population 1,250, anticipated federal compensation of $18,000, only to receive $76,000: “When the Select Board saw that unbudgeted income was actually coming, we then lowered the municipal property tax rate by 2 cents,” it reports.

Overall, Vermont citizens and communities so far have reaped almost $170 million in FEMA money and almost that much more in funds from the Federal Highway Administration and other government agencies. If filling out the accompanying paperwork isn’t enough, many localities also are writing new flood plain regulations to qualify for the National Flood Insurance Program.

“Irene was a wake-up call,” writes the Select Board in West Fairlee, population 652. “Most natural disasters are localized and not eligible for state or FEMA relief funds. We must ensure that the highway capital fund maintains an emergency balance to protect us in the future.”

Local leaders in Chester, population 3,154, simply are thankful for finally paying off their Irene debt — and dodging another set of bills: “It would be an understatement to say we were very fortunate that Hurricane Sandy missed our community at the end of last year, and we are no doubt grateful,” they conclude, “but we certainly sympathize with those areas that were affected by that horrific storm.”